Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014102.1 Corchorus capsularis cultivar CVL-1 contig14123, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 52621
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2632 original size:23 final size:23
Alignment explanation
Indices: 2592--2636 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2582 GTTCGATAAA
*
2592 TGTTCATTTATTAGCTCGTTTAT
1 TGTTCATTTAATAGCTCGTTTAT
2615 TGTTCATTTAAATA-CTCGTTTA
1 TGTTCATTT-AATAGCTCGTTTA
2637 AAATTCGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (23 bp):
TGTTCATTTAATAGCTCGTTTAT
Found at i:9972 original size:22 final size:22
Alignment explanation
Indices: 9947--10349 Score: 235
Period size: 22 Copynumber: 18.4 Consensus size: 22
9937 GATGTAATAG
* *
9947 AAATTTCATTAGGAGGTTATCC
1 AAATTTCATAAGGAGGTTATCA
* *
9969 AAATTTAAT-AGTGTGGTTATCA
1 AAATTTCATAAG-GAGGTTATCA
* *
9991 AAATTTC--AAGCAAGATTATCA
1 AAATTTCATAAG-GAGGTTATCA
10012 AAATTAT-ATAAGGAGGTTATCA
1 AAATT-TCATAAGGAGGTTATCA
* *
10034 AAATTTCA-CAGTGTGGTTATCA
1 AAATTTCATAAG-GAGGTTATCA
* * *
10056 AAATTTCATGA-TATGGTTACCA
1 AAATTTCATAAGGA-GGTTATCA
*
10078 AAATTTCATAAGGAAGTTATC-
1 AAATTTCATAAGGAGGTTATCA
* * *
10099 -AATTTGAT-AGTGTGCTTA-CTA
1 AAATTTCATAAG-GAGGTTATC-A
**
10120 AAATTTCATACCGATGG-TATCA
1 AAATTTCATAAGGA-GGTTATCA
10142 AAATTTCATAAGGAGGTTATCA
1 AAATTTCATAAGGAGGTTATCA
* * *
10164 AAGTTTTTATATGGAGGTTATCA
1 AA-ATTTCATAAGGAGGTTATCA
* **
10187 AAATTTCATACGGAATTTATCA
1 AAATTTCATAAGGAGGTTATCA
*
10209 AAATTTCA-AAGGGAAGTTATCA
1 AAATTTCATAA-GGAGGTTATCA
* *
10231 AAATTTCAT-AGTGTGATTATCA
1 AAATTTCATAAG-GAGGTTATCA
* * *
10253 AATTTTTAT-AGCAAGGTTATCA
1 AAATTTCATAAG-GAGGTTATCA
* *
10275 AAATTTAAT-AGTGTGGTTATCAA
1 AAATTTCATAAG-GAGGTTATC-A
** * *
10298 AAATTTCATTTGCAAGTTATCA
1 AAATTTCATAAGGAGGTTATCA
*
10320 AAA-TTCTATAAGAAGGTTATCA
1 AAATTTC-ATAAGGAGGTTATCA
10342 AAATTTCA
1 AAATTTCA
10350 AGGATAATTG
Statistics
Matches: 291, Mismatches: 64, Indels: 52
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.01
20 11 0.04
21 26 0.09
22 206 0.71
23 44 0.15
24 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
AAATTTCATAAGGAGGTTATCA
Found at i:9995 original size:44 final size:43
Alignment explanation
Indices: 9917--10353 Score: 265
Period size: 44 Copynumber: 10.0 Consensus size: 43
9907 GTCTATGTGT
* * *
9917 GGTTAACAAAATTTCATACTGAT-GTAAT-AGAAATTTCATTAGGA
1 GGTTATCAAAATTTCATAGTG-TGGTTATCA-AAATTTCA-TAGGA
* * *
9961 GGTTATCCAAATTTAATAGTGTGGTTATCAAAATTTCA-AGCAA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAG-GA
* * * *
10004 GATTATCAAAATTAT-ATAAG-GAGGTTATCAAAATTTCACAGTGT
1 GGTTATCAAAATT-TCAT-AGTGTGGTTATCAAAATTTCATAG-GA
* *
10048 GGTTATCAAAATTTCAT-GATATGGTTACCAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATAG-TGTGGTTATCAAAATTTCAT-AGGA
* * * *
10092 AGTTATC--AATTTGATAGTGTGCTTA-CTAAAATTTCATACCGA
1 GGTTATCAAAATTTCATAGTGTGGTTATC-AAAATTTCATA-GGA
* * *
10134 TGG-TATCAAAATTTCATAAG-GAGGTTATCAAAGTTTTTATATGGA
1 -GGTTATCAAAATTTCAT-AGTGTGGTTATCAAA-ATTTCATA-GGA
*** *
10179 GGTTATCAAAATTTCATACG-GAATTTATCAAAATTTCAAAGGGA
1 GGTTATCAAAATTTCATA-GTGTGGTTATCAAAATTTCATA-GGA
* * * * *
10223 AGTTATCAAAATTTCATAGTGTGATTATCAAATTTTTATAGCAA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAG-GA
* * *
10267 GGTTATCAAAATTTAATAGTGTGGTTATCAAAAATTTCATTTGCA
1 GGTTATCAAAATTTCATAGTGTGGTTATC-AAAATTTCA-TAGGA
* **
10312 AGTTATCAAAA-TTCTATAAG-AAGGTTATCAAAATTTCA-AGGA
1 GGTTATCAAAATTTC-AT-AGTGTGGTTATCAAAATTTCATAGGA
10354 TAATTGCTCA
Statistics
Matches: 308, Mismatches: 58, Indels: 56
0.73 0.14 0.13
Matches are distributed among these distances:
41 2 0.01
42 34 0.11
43 37 0.12
44 165 0.54
45 66 0.21
46 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGA
Found at i:10183 original size:131 final size:128
Alignment explanation
Indices: 9947--10305 Score: 333
Period size: 131 Copynumber: 2.7 Consensus size: 128
9937 GATGTAATAG
* * *
9947 AAATTTCATTAGGAGGTTATCCAAATTTAATAGTGTGGTTATCAAAATTTCAAGCAAGATTATCA
1 AAATTTCATAAGGAAGTTAT-CAAATTTAATAGTGTGCTTATCAAAATTTCAAGCAAGATTATCA
*
10012 AAATTATATAAGGAGGTTATCAAAATTTCACAGTGTGGTTATCAAAATTTCAT-GATATGGTTAC
65 AAATTATATAAGGAGGTTATCAAAATTTCACAGTGAGGTTATCAAAATTTCATAGA-AT--TTAC
10076 CA
127 CA
* *
10078 AAATTTCATAAGGAAGTTATC-AATTTGATAGTGTGCTTA-CTAAAATTTCATA-C-CGATGGTA
1 AAATTTCATAAGGAAGTTATCAAATTTAATAGTGTGCTTATC-AAAATTTCA-AGCAAGAT--TA
* * *
10139 TCAAAATT-TCATAAGGAGGTTATCAAAGTTTTTATA-TGGAGGTTATCAAAATTTCATACGGAA
62 TCAAAATTAT-ATAAGGAGGTTATCAAA-ATTTCACAGT-GAGGTTATCAAAATTTCATA--GAA
*
10202 TTTATCA
122 TTTACCA
* * * * *
10209 AAATTTCA-AAGGGAAGTTATCAAAATTTCATAGTGTGATTATCAAATTTTTATAGCAAGGTTAT
1 AAATTTCATAA-GGAAGTTATC-AAATTTAATAGTGTGCTTATCAAAATTTCA-AGCAAGATTAT
*
10273 CAAAATT-TA-ATAGTGTGGTTATCAAAAATTTCA
63 CAAAATTATATA-AG-GAGGTTATC-AAAATTTCA
10306 TTTGCAAGTT
Statistics
Matches: 190, Mismatches: 19, Indels: 36
0.78 0.08 0.15
Matches are distributed among these distances:
128 4 0.02
129 27 0.14
130 32 0.17
131 65 0.34
132 3 0.02
133 50 0.26
134 7 0.04
135 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (128 bp):
AAATTTCATAAGGAAGTTATCAAATTTAATAGTGTGCTTATCAAAATTTCAAGCAAGATTATCAA
AATTATATAAGGAGGTTATCAAAATTTCACAGTGAGGTTATCAAAATTTCATAGAATTTACCA
Found at i:10831 original size:22 final size:22
Alignment explanation
Indices: 10783--10881 Score: 71
Period size: 22 Copynumber: 4.6 Consensus size: 22
10773 TTCATAATGT
*
10783 GGTTATCAAATTTTTATAGAGA
1 GGTTATCAAAATTTTATAGAGA
*
10805 AGTTATCAAAATTTTATAGCA-A
1 GGTTATCAAAATTTTATAG-AGA
* * *
10827 GGTTATC---ATTTCATAGGGT
1 GGTTATCAAAATTTTATAGAGA
* * * * *
10846 GATTATTATAATTTCATATAGA
1 GGTTATCAAAATTTTATAGAGA
10868 GGTTATCAAAATTT
1 GGTTATCAAAATTT
10882 AGTGGTGTGT
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
19 13 0.22
22 44 0.76
23 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.41
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGAGA
Found at i:11018 original size:22 final size:22
Alignment explanation
Indices: 10958--11018 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
10948 GGGATTGAGA
10958 TTATCAAAATTTCAT-ATGAAAG
1 TTATCAAAATTTCATAATG-AAG
*
10980 TTATCAAAATATT-ATAATG-TG
1 TTATCAAAAT-TTCATAATGAAG
11001 TTTATCAAAATTTCATAA
1 -TTATCAAAATTTCATAA
11019 GGATATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 3 0.09
22 26 0.76
23 5 0.15
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGAAG
Found at i:11493 original size:10 final size:10
Alignment explanation
Indices: 11475--11516 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
11465 ACTAGTAGTT
11475 ATATAAAAAA
1 ATATAAAAAA
11485 ATATCAAAAAA
1 ATAT-AAAAAA
11496 AT-TAAAACAA
1 ATATAAAA-AA
11506 ATA-AAAAAA
1 ATATAAAAAA
11515 AT
1 AT
11517 TTCAACCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.28
10 13 0.45
11 8 0.28
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (10 bp):
ATATAAAAAA
Found at i:15934 original size:42 final size:42
Alignment explanation
Indices: 15854--15936 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
15844 AAGGGATCGC
* *
15854 ACATGACCGGTCATTGAATGGGGCAACCACACAAGACCGGGT
1 ACATGACCGGCCATTGAATGGAGCAACCACACAAGACCGGGT
* * *
15896 ACATGACCGGCCA-TGACATGGAGCAATCGCACATGACCGGG
1 ACATGACCGGCCATTGA-ATGGAGCAACCACACAAGACCGGG
15937 CACAACCCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.30, C:0.28, G:0.29, T:0.13
Consensus pattern (42 bp):
ACATGACCGGCCATTGAATGGAGCAACCACACAAGACCGGGT
Found at i:21246 original size:8 final size:8
Alignment explanation
Indices: 21233--21266 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
21223 CACCTTCTTG
21233 AAAAATTC
1 AAAAATTC
21241 AAAAATTC
1 AAAAATTC
*
21249 AGAAACTTC
1 A-AAAATTC
21258 AAAAATTC
1 AAAAATTC
21266 A
1 A
21267 TAGCTGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:22883 original size:33 final size:33
Alignment explanation
Indices: 22846--22954 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 33
22836 TGATACTAAA
* * *
22846 TCTGTTTTGGATGCTAATTGTCA-TGAAAATAAT
1 TCTGTTTTGGTTGATAATAG-CATTGAAAATAAT
* *
22879 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATAATAGCATTGAAAATAAT
*
22912 TCTGTTTTGGTTGATTATAGCATTGAAAATAAT
1 TCTGTTTTGGTTGATAATAGCATTGAAAATAAT
22945 TCTGTTTTGG
1 TCTGTTTTGG
22955 GTGAAAAGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 2 0.03
33 66 0.97
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATAATAGCATTGAAAATAAT
Found at i:37516 original size:51 final size:51
Alignment explanation
Indices: 37435--37541 Score: 169
Period size: 51 Copynumber: 2.1 Consensus size: 51
37425 CCTATCGCTT
* *
37435 CATCACCACTTTTAGTGTAGTAAACACTTTCGGTGCCATCATCTTCGGTGC
1 CATCACCACTTTCAGTGTAGTAAACACTTTCGGTGCCATCACCTTCGGTGC
* * *
37486 CATCGCCACTTTCAGTGTAGTAAACACTTTCGGTGCCATTACCTTGGGTGC
1 CATCACCACTTTCAGTGTAGTAAACACTTTCGGTGCCATCACCTTCGGTGC
37537 CATCA
1 CATCA
37542 TCTCCGGTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (51 bp):
CATCACCACTTTCAGTGTAGTAAACACTTTCGGTGCCATCACCTTCGGTGC
Found at i:38794 original size:18 final size:18
Alignment explanation
Indices: 38768--38840 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 18
38758 TGTTGAACAA
* *
38768 GTGCAGCCAATTGGTGCG
1 GTGCAGCCACTTGGTGTG
*
38786 GTGCGGCCACTTGGTGTG
1 GTGCAGCCACTTGGTGTG
* *
38804 GTGCAACCACTTGGTGTA
1 GTGCAGCCACTTGGTGTG
* *
38822 GTGCGGCCACTGGGTGTG
1 GTGCAGCCACTTGGTGTG
38840 G
1 G
38841 CGCCTGGTGC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.12, C:0.22, G:0.41, T:0.25
Consensus pattern (18 bp):
GTGCAGCCACTTGGTGTG
Found at i:38818 original size:36 final size:36
Alignment explanation
Indices: 38768--38840 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
38758 TGTTGAACAA
* * *
38768 GTGCAGCCAATTGGTGCGGTGCGGCCACTTGGTGTG
1 GTGCAACCAATTGGTGCAGTGCGGCCACTGGGTGTG
* *
38804 GTGCAACCACTTGGTGTAGTGCGGCCACTGGGTGTG
1 GTGCAACCAATTGGTGCAGTGCGGCCACTGGGTGTG
38840 G
1 G
38841 CGCCTGGTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.12, C:0.22, G:0.41, T:0.25
Consensus pattern (36 bp):
GTGCAACCAATTGGTGCAGTGCGGCCACTGGGTGTG
Found at i:42171 original size:16 final size:16
Alignment explanation
Indices: 42150--42181 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42140 GAACCTCGGG
*
42150 TTTTCGGGTTTGGGTC
1 TTTTCGGGTTCGGGTC
42166 TTTTCGGGTTCGGGTC
1 TTTTCGGGTTCGGGTC
42182 GTTACAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.38, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTC
Found at i:43465 original size:16 final size:16
Alignment explanation
Indices: 43438--43512 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
43428 GTCGGGTTGA
43438 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTCATT
* *
43454 TTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCATT
*
43470 TCGGGTTCGGGTCGTT
1 TCGGGTTCGGGTCATT
* * *
43486 T-GGATTCAGGTAATT
1 TCGGGTTCGGGTCATT
43501 TCGGGTTCGGGT
1 TCGGGTTCGGGT
43513 ACCCAAAAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
15 11 0.23
16 36 0.77
ACGTcount: A:0.08, C:0.13, G:0.39, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:43502 original size:31 final size:32
Alignment explanation
Indices: 43438--43512 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
43428 GTCGGGTTGA
* * ** *
43438 TCGGGTTCGGGTCATTTTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCAGTTTGGATTCAGGTAATT
43470 TCGGGTTCGGGTC-GTTTGGATTCAGGTAATT
1 TCGGGTTCGGGTCAGTTTGGATTCAGGTAATT
43501 TCGGGTTCGGGT
1 TCGGGTTCGGGT
43513 ACCCAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 25 0.66
32 13 0.34
ACGTcount: A:0.08, C:0.13, G:0.39, T:0.40
Consensus pattern (32 bp):
TCGGGTTCGGGTCAGTTTGGATTCAGGTAATT
Done.